Steve Clarke’s side took a shock lead through Ryan Christie’s first half goal at the Stadion Maksimir.
But Igor Matanovic equalised before the interval and Kramaric bagged the winner midway through the second half.
Scotland have lost four successive games for the first time since 2019.
They arrived in Zagreb winless in their last eight competitive matches, the longest streak in their history, and that dismal run has now reached nine.
Scotland have mustered just one win in their last 15 matches, a 2-0 victory over minnows Gibraltar in June.
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